SNOMED CT与基本形式本体——标准趋同还是矛盾?“临床发现”案例

IF 2.5 4区 计算机科学 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE
Applied Ontology Pub Date : 2023-08-31 DOI:10.3233/ao-230018
Stefan Schulz, James T. Case, Peter Hendler, Daniel Karlsson, Michael Lawley, Ronald Cornet, Robert Hausam, Harold Solbrig, Karim Nashar, Catalina Martínez-Costa, Yongsheng Gao
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引用次数: 0

摘要

背景:SNOMED CT是一个大型术语系统,旨在代表医疗保健的各个方面。它目前的形式和内容是几十年自下而上发展的结果。由于SNOMED CT的形式化描述,它可以被认为是一个本体。基本形式本体论(BFO)是一种基础本体论,它提出了一小组不相交的、层次有序的类,并由关系和公理支持。相比之下,作为一种典型的自上而下的努力,BFO被设计为自然科学和相关学科领域本体论的基础框架。尽管大多数人认为领域本体应该作为基础本体的扩展来创建,但众所周知,对正在使用的合并领域本体(如SNOMED CT)进行事后协调是具有挑战性的。方法:我们探讨了将SNOMED CT与BFO相协调的可行性,重点是SNOMED CT临床发现层次。它拥有超过100000个课程,约占SNOMED CT内容的三分之一。特别地,我们在BFO下使用描述逻辑来表示典型的SNOMED CT发现/紊乱概念。创建了三种表征模式,并分析了其中的逻辑蕴涵。结果:在第一次审查下,疾病、障碍、体征和症状形成一个同质的本体论上层类别的临床直觉似乎与BFO对延续和发生的上层区分不相容。临床发现类似乎是临床感兴趣的各种实体的保护伞,如物质实体、过程、状态、处置和质量。这表明,从BFO的角度来看,临床发现并不是一个合适的高级分类。在仔细检查该层次结构中的分类联系及其隐含含义时,很明显,临床发现类别并不是字面意义上的实体(如骨折、过敏、肿瘤、疼痛、出血、癫痫发作、发烧)的特征,而是骨折、过敏和疼痛等患者的状况。这说明了临床发现层次结构的当前特征,其中复杂类被建模为其组成部分的子类。这些分类联系中的大多数是推断出来的,这是“角色组”设计模式的结果,这种模式在SNOMED CT中普遍存在,并且在其语义方面经常受到争议。结论:我们的分析得到了以下建议:(i)将SNOMED CT的“角色群”性质等同于自反和传递的BFO关系“有发生部分”;以及(ii)将临床发现重新解释为临床发生,即生物体中的时间扩展实体,具有一个或多个作为连续发生的时间部分的发生。这种重新解释得到了《临床发现》下类别的手动分析以及其他本体中类似建模模式的识别的证实。因此,SNOMED CT不需要任何内容重新设计来建立与BFO的兼容性,除了这种重新解释和建议的重新标记。关于事后协调术语与原则性基础本体的可行性,我们的研究结果支持这样一种假设,即这不一定需要重大的重新设计工作,而是对术语管理者和用户的隐含假设进行仔细分析。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
SNOMED CT and Basic Formal Ontology – convergence or contradiction between standards? The case of “clinical finding”
Background: SNOMED CT is a large terminology system designed to represent all aspects of healthcare. Its current form and content result from decades of bottom-up evolution. Due to SNOMED CT’s formal descriptions, it can be considered an ontology. The Basic Formal Ontology (BFO) is a foundational ontology that proposes a small set of disjoint, hierarchically ordered classes, supported by relations and axioms. In contrast, as a typical top-down endeavor, BFO was designed as a foundational framework for domain ontologies in the natural sciences and related disciplines. Whereas it is mostly assumed that domain ontologies should be created as extensions of foundational ontologies, a post-hoc harmonization of consolidated domain ontologies in use, such as SNOMED CT, is known to be challenging. Methods: We explored the feasibility of harmonizing SNOMED CT with BFO, with a focus on the SNOMED CT Clinical Finding hierarchy. With more than 100,000 classes, it accounts for about one third of SNOMED CT’s content. In particular, we represented typical SNOMED CT finding/disorder concepts using description logics under BFO. Three representational patterns were created and the logical entailments analyzed. Results: Under a first scrutiny, the clinical intuition that diseases, disorders, signs and symptoms form a homogeneous ontological upper-level class appeared incompatible with BFO’s upper-level distinction into continuants and occurrents. The Clinical finding class seemed to be an umbrella for all kinds of entities of clinical interest, such as material entities, processes, states, dispositions, and qualities. This suggests the conclusion that Clinical finding would not be a suitable upper-level class from an BFO perspective. On closer inspection of the taxonomic links within this hierarchy and the implicit meaning derived thereof, it became clear that Clinical finding classes do not characterize the entity (e.g. a fracture, allergy, tumor, pain, hemorrhage, seizure, fever) in a literal sense but rather the condition of a patient having that fracture, allergy, pain etc. This gives sense to the current characteristic of the Clinical Finding hierarchy, in which complex classes are modeled as subclasses of their constituents. Most of these taxonomic links are inferred, as the consequence of the ‘role group’ design pattern, which is ubiquitous in SNOMED CT and has often been subject of controversy regarding its semantics. Conclusion: Our analyses resulted in the proposal of (i) equating SNOMED CT’s ‘role group’ property with the reflexive and transitive BFO relation ‘has occurrent part’; and (ii) reinterpreting Clinical Findings as Clinical Occurrents, i.e. temporally extended entities in an organism, having one or more occurrents as temporal parts that occur in continuants. This re-interpretation was corroborated by a manual analysis of classes under Clinical Finding, as well as the identification of similar modeling patterns in other ontologies. As a result, SNOMED CT does not require any content redesign to establish compatibility with BFO, apart from this re-interpretation, and a suggested re-labeling. Regarding the feasibility of harmonizing terminologies with principled foundational ontologies post-hoc, our results provide support to the assumption that this does not necessarily require major redesign efforts, but rather a careful analysis of the implicit assumptions of terminology curators and users.
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来源期刊
Applied Ontology
Applied Ontology COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE-COMPUTER SCIENCE, INFORMATION SYSTEMS
CiteScore
4.80
自引率
30.00%
发文量
15
审稿时长
>12 weeks
期刊介绍: Applied Ontology focuses on information content in its broadest sense. As the subtitle makes clear, two broad kinds of content-based research activities are envisioned: ontological analysis and conceptual modeling. The former includes any attempt to investigate the nature and structure of a domain of interest using rigorous philosophical or logical tools; the latter concerns the cognitive and linguistic structures we use to model the world, as well as the various analysis tools and methodologies we adopt for producing useful computational models, such as information systems schemes or knowledge structures. Applied Ontology is the first journal with explicit and exclusive focus on ontological analysis and conceptual modeling under an interdisciplinary view. It aims to establish a unique niche in the realm of scientific journals by carefully avoiding unnecessary duplication with discipline-oriented journals. For this reason, authors will be encouraged to use language that will be intelligible also to those outside their specific sector of expertise, and the review process will be tailored to this end. For example, authors of theoretical contributions will be encouraged to show the relevance of their theory for applications, while authors of more technological papers will be encouraged to show the relevance of a well-founded theoretical perspective. Moreover, the journal will publish papers focusing on representation languages or algorithms only where these address relevant content issues, whether at the level of practical application or of theoretical understanding. Similarly, it will publish descriptions of tools or implemented systems only where a contribution to the practice of ontological analysis and conceptual modeling is clearly established.
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